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- PDB-4lgi: N-terminal truncated NleC structure -

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Basic information

Entry
Database: PDB / ID: 4lgi
TitleN-terminal truncated NleC structure
ComponentsUncharacterized protein
KeywordsHYDROLASE / metallopeptidases / a type III secretion protease
Function / homologyNFkB-p65-degrading zinc protease / NFkB-p65-degrading zinc protease / metal ion binding / T3SS secreted effector NleC
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.301 Å
AuthorsLi, W.Q. / Liu, Y.X. / Sheng, X.L. / Yan, C.Y. / Wang, J.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure and mechanism of a type III secretion protease, NleC
Authors: Li, W. / Liu, Y. / Sheng, X. / Yin, P. / Hu, F. / Liu, Y. / Chen, C. / Li, Q. / Yan, C. / Wang, J.
History
DepositionJun 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)120,4534
Polymers120,4534
Non-polymers00
Water4,558253
1
A: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)60,2272
Polymers60,2272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-7 kcal/mol
Surface area18770 Å2
MethodPISA
2
B: Uncharacterized protein
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)60,2272
Polymers60,2272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-6 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.512, 88.664, 110.653
Angle α, β, γ (deg.)90.00, 92.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein


Mass: 30113.354 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ECs0847, Z0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8X834
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.18 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: evaporation / pH: 6
Details: 0.2M (NH4)2SO4, 100mM MES pH 6.0, 20%(w/v) polyethylene glycol 3000, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 100152 / Num. obs: 98250 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.38 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.301→37.607 Å / SU ML: 0.35 / σ(F): 0.94 / Phase error: 29.65 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 4981 5.07 %RANDOM
Rwork0.2527 ---
obs0.2541 98165 97.93 %-
all-100239 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.44 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.1525 Å2-0 Å2-1.8977 Å2
2---10.4035 Å20 Å2
3---0.894 Å2
Refinement stepCycle: LAST / Resolution: 2.301→37.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6548 0 0 253 6801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136672
X-RAY DIFFRACTIONf_angle_d1.2269047
X-RAY DIFFRACTIONf_dihedral_angle_d18.4572405
X-RAY DIFFRACTIONf_chiral_restr0.097989
X-RAY DIFFRACTIONf_plane_restr0.0051209
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.301-2.32720.31381740.3285298993
2.3272-2.35450.30741660.3213305598
2.3545-2.38320.33241880.3075313399
2.3832-2.41340.36551470.3072313199
2.4134-2.44520.32861620.3093318199
2.4452-2.47860.41351730.3143322499
2.4786-2.51410.37571780.30583134100
2.5141-2.55160.32911610.293309599
2.5516-2.59140.30381870.2815316599
2.5914-2.63390.33241750.28693100100
2.6339-2.67930.34271520.28763188100
2.6793-2.7280.3231800.2802317599
2.728-2.78050.32781390.2781315199
2.7805-2.83720.26521780.2664319499
2.8372-2.89890.30341750.26193102100
2.8989-2.96630.30871850.27253207100
2.9663-3.04040.26131380.2733312299
3.0404-3.12260.29351620.2684316099
3.1226-3.21440.31151840.261309799
3.2144-3.31810.26561640.2524320299
3.3181-3.43670.31211560.2542310999
3.4367-3.57410.31061550.2368312198
3.5741-3.73670.26171610.2321314298
3.7367-3.93350.24622000.2108304297
3.9335-4.17960.21331720.2123301196
4.1796-4.50190.23951470.2155293692
4.5019-4.9540.21161350.2166293691
4.954-5.66870.2621390.2508304395
5.6687-7.1340.28752010.2728304398
7.134-37.61160.25271470.2278299694
Refinement TLS params.Method: refined / Origin x: -5.0082 Å / Origin y: -19.5623 Å / Origin z: 25.217 Å
111213212223313233
T0.2306 Å2-0.0014 Å20.021 Å2-0.1792 Å2-0.0066 Å2--0.2366 Å2
L0.2291 °20.097 °20.1955 °2-0.2249 °20.0926 °2--0.5899 °2
S0.03 Å °-0.0182 Å °-0.0473 Å °0.0388 Å °-0.0213 Å °-0.0281 Å °-0.0198 Å °0.0367 Å °-0.024 Å °
Refinement TLS groupSelection details: all

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